A/N:

Lots of people liked the idea of dark!John, so here it is. I'm not 100% sure where this story is going yet. Before you read further, know that this is a *very* M story. There are BDSM themes, sex + violence, and likely some non-consent. John and Molly are not in good shape here, and they're gonna take it out on Sherlock, and each other.

Had a hard time defining this story's category. A combo of hurt/comfort/angst was the best I could come up with, but I'm not sure how well it fits. Apologies ahead of time if this doesn't turn out to be what you're looking for. If you reviewed my last story and agreed that dark!John would be awesome, this is exactly what you're looking for.

The title is a play on "The Empty House," the story that marks the return of Sherlock Holmes after his "death" in the canon stories.

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Ch 1

The only thing that thrilled John Watson anymore was a fresh body. As it turned out (once Sherlock was gone and he had no choice but to go back to work full time) John was a terrible general practitioner. It was boring. When Molly mentioned to him that there was an opening at the morgue, he felt he had little choice but to switch career paths.

Working crime scenes were interesting. He tried to examine everything with the same eye as Sherlock once had. He couldn't always solve the crime, but he could tell Lestrade how the victim had died, and in the course of two years he had helped close almost fifty cases.

The body on the slab in front of him was a Jane Doe, aged nineteen to twenty-five years. Signs of sexual assault, severe bruising, fractured skull. You didn't need to be a doctor to know how this one had died. John pulled off his bloody gloves and spoke into his tape recorder. "Cause of death, internal bleeding due to blunt force trauma. Boring."

"Did you just call that dead girl boring?" Molly entered the room with two coffee mugs.

John accepted his mug and swallowed down the too-hot liquid without tasting it. He didn't care about coffee, but found caffeine to be invaluable. "Where's the mystery Molly, where's the challenge?"

"The mystery is how you became such a tosser," Molly said, even though they both knew it was no mystery at all. "The darts club is meeting tonight. You should come."

"I'm working," John said, and wheeled Jane Doe back into the cooler.

"You're always working."

"The Work is all that matters," John replied.

"Don't do that," Molly said, her voice growing irritated quickly. "I hate it when you do that. Don't channel him. It's been three years John. Let it go."

John let out a sharp laugh. Three years and neither of them had let it go. John grew more sullen, and Molly more bitter with every day that passed. John never expected his grief to lessen, but he thought in time Molly would heal and move on. Instead she just got angry. He couldn't blame her. He was often angry at the memory of Sherlock as well. Anger was just a part of life without Sherlock.

"Come play darts," Molly tried again. "You get to throw sharp pointy things at a wall—that must make you feel good inside. I know it makes me feel warm and fuzzy all over." She nearly purred this, leaning into John. This wasn't a new behavior with her—they'd hooked up multiple times over the years, even during John's tragic marriage to Mary.

Mrs. Hudson had quickly tired of his moods. Lestrade was patient and indulgent (which could be infuriating), and Mary had only ever pretended to understand John's refusal to get over Sherlock's death. Molly was the only one who seemed to be capable of giving him what he needed, and she seemed pretty content with what he gave her as well.

John let Molly lean up against him. He wrapped an arm around her, sliding his hand up under her jumper and letting it slide across the smooth skin of her stomach. It was getting late, but not late enough. There were still plenty of people wandering the hospital. It would not be a good idea to—she leaned up and bit his earlobe.

Well, John wasn't known for his good ideas.

He took the coffee out of her hand and set their mugs down on the counter before dragging Molly off to the large walk-in cooler that dominated the room. Three bodies were lined up on gurneys in body bags, including the girl who had been killed in a sexual assault. Both were fully aware of this when John bent Molly over on an empty gurney and pushed her skirt up around her waist. She wasn't wearing panties—too much of a bother. He stroked her smooth skin before bringing his open palm down hard across her ass.

The walls of the cooler muffled the sound when she cried out—a necessity when carrying on these sorts of activities in the workplace. He enjoyed the feeling of flesh hitting flesh, of her ass growing hot and rosy as he spanked her. This was tame for the two if them but Molly screamed anyway, her cries soon disintegrating into a whining moan as her arousal grew, and she spread her legs in an attempt for him to notice that there were warmer, more moist places he could be focusing on

John's cock was always rock hard at this point, and he only needed one hand to free himself and plunge into her cunt. Molly's moan's were very appreciative, and John grabbed her by the hips and thrust hard and fast. They never lasted long in the cooler. It was cold in there, after all. Most of the time Molly didn't even bother with her own orgasm, and John wasn't too concerned with giving her one. He came fast and hard within a minute, inside her so it was a mess that she would have to deal with instead of him.

He exited the cooler first and was already at the work table, getting together the tissue samples from Jane Doe. "These need to go down to pathology," he said when Molly re-joined him, not looking the least bit rumpled but walking a bit stiffly.

"Just let me run to the loo-" she said, but he thrust the containers into her hands. Her eyes were on fire when she glared at him, but she bit back whatever she wanted to say to him. "Or I could just do it now."

"An excellent decision."

She turned to leave and he watched her walk, enjoying the way she kept her legs clenched together all the way to the knees, anything to prevent his cum from leaking down her legs in the hall. Molly. Ah, she was wonderful. She let him do whatever he wanted to her, and it made them both feel better. He wished he could love her. But he couldn't love anyone. Not with Sherlock gone.

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Sherlock Holmes stood on the exact spot where he had "died" three years previous, and stared at the hospital entrance. Was it interesting or troubling that John had taken a job at the same building where Sherlock had seemingly fallen to his death? It was troubling to be there again after three years on the run. Three years eliminating Moriarty's underlings, assuring that John, Mrs. Hudson and Lestrade were safe. If only they knew what he had done for them.

Three years without a friend in the world, and he finally understood what friendship really was. It was sacrificing everything.

Everything.

His enemies were dead, they were safe, and he was ready to come home. His first instinct was not to return to Baker Street—it was to find John. This didn't surprise him at all. Three years of contemplation and loneliness had done a lot for him. He had done some soul-searching, and he discovered something remarkable and unexpected.

He had a soul.

He was as human as the rest of them after all and his soul pined for John. They way he took care of him, his sense of humor, the way he always considered Sherlock to be amazing when no one else believed in him. Once he was on his own it hadn't taken him long to realize that John had loved him, and he loved John back.

Sherlock shivered as he stepped over his death site and headed towards the front doors of the hospital, adrenaline burning through his veins. He was going to see John again, and he would tell him he had been an idiot, he would tell him that he was sorry, and that he loved him. John was his best friend, his only friend, and he loved him so, so very much.

He walked quickly, his excitement urging him forward at some speed. He wasn't even looking, just thinking, and he slammed hard into a person leaving the hospital, the impact such that the both of them fell to the ground.

"I am so, so sorry," the man said, scrambling quickly to his feet and reaching to help Sherlock to his feet. The world turned sideways and he nearly fell to the ground again. John. It was his John.

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John reached out to help the old man to his feet. The last thing he needed was to bowl over geriatric strangers and get sued. "I am so sorry," he said, grasped the old chap's hand. His grip was stronger than he expected, and it relived John a bit of his worry. "Are you alright?"

The man was tall, or would be if he wasn't bent over with a cane, grey haired and bearded, his face half-obscured by a hat and a flipped coat collar. "Quite-quite alright." He seemed a little breathless.

"Okay, good then." He hurried on his way, just out for a quick bite and then back to work. There was no more crime for the day, but there was another autopsy—a thirty-five year old man who had dropped dead for no apparent reason after a jog. Likely it was an undiagnosed heart condition, but John didn't want to rule out anything a bit more interesting.

He forgot about the man he knocked over while standing in line at the sandwich shop, and thought nothing more of him while he ate and walked back to work. It was a shock and an annoyance when he found the same man standing in his lab.

"Can I help you?" he asked.

"I hope so, Doctor Watson."

Wonderful, so he knew his name. John just wanted to get back to work, so he walked past the man to the cooler, hoping a nice fresh corpse would scare the visitor away. "I'm really busy," he said as he wheeled the gurney out. "So if we could-"

The old man was gone. In his place stood a ghost.

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End Notes: Dunno how probable it is for an army doctor to switch to medical examiner in the course of a few years, but it's just fanfic and I dont give a crap.